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Aligning these sequences to a selection of sequences from insects revealed some degree of conservation (a few stretches of conserved amino acids) indicating similar functions.
A possible example is shown in Figure 11 in an alignment of a selection of sequences of TRANSFAC motif M00912 bound by the mammalian transcription factor C/EBP, which forms a leucine zipper homodimer.
To characterize and compare the outbreak viral sequences, we used as reference material a selection of sequences from strains obtained 2 or 3 years earlier in the same ecogeographic region near Corral.
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Pairwise alignment was used to compare a selection of eliminated sequences with known MS4A protein sequences to verify that CDART accurately removed nonconserved proteins.
All remaining sequences were mapped to a selection of genomic sequences to determine whether there is evidence for an associated hairpin structure characteristic of miRNAs, either in barley or in related genomes.
We then made a preliminary neighbour-joining tree with the 244 used sequences in order to make a selection of representative sequences to be included in a maximum likelihood tree.
To evaluate the sequence relationships among mastrevirus genomes, a selection of mastrevirus sequences available at the time was obtained [see Additional file 2].
The genotyping of NoV strains was obtained by sequence analysis performed on the RNA-dependent RNA polymerase gene and the sequences were aligned and compared with a selection of representative sequences from the various NoV genotypes available in online databases (12 ).
All human H1N1 viruses with publicly available, full-length sequences of the hemagglutinin subunit HA1 from 1918 to 1957, and a selection of representative sequences from every year thereafter including the 2009 novel H1N1 were studied (see Additional File 2 for list and accession numbers).
A selection of 24 APOBEC1 (A1) sequences (21 Eutheria species, two Metatheria and one Aves species) and 34 Activation induced cytidine deaminases (AICDA) sequences (23 Eutheria species, three Metatheria, one Prototheria, two Aves, two Amphibia and three Actinopterygii species) and were used as outgroups.
A comprehensive collection of new BVDV sequences from all cattle breeding areas in Italy was investigated by phylogenetic analysis and compared against a selection of reference sequences of known genotypes and subtypes retrieved from public genetic databases.
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